The dynamic epitranscriptome: Control of mRNA fate and function by nucleotide modifications

The fate and function of each mRNA is determined by both its nucleotide sequence, as well as by its “epitranscriptomic code.” This code refers to the presence and distribution of methylation marks in the transcript. The discovery of the epitranscriptomic code was made possible by our initial development of MeRIP‐Seq, a method for mapping N 6 ‐methyladenosine (m 6 A) throughout the transcriptome. MeRIP‐Seq revealed that m 6 A is found in at least 25% of mRNAs in the transcriptome, differentially expressed in development and disease, and enriched in specific regions of the transcript body. The second most prevalent modified nucleotide in mRNA is N 6 ,2′‐ O ‐dimethyladenosine (m 6 A m ), which is exclusively located adjacent to the 7‐methylguanosine‐cap at the first encoded nucleotide in up to 40% of mRNAs. This modification is formed when adenosine residues at the first encoded nucleotide position in mRNAs are constitutively modified with a single methyl modification to form 2′‐ O ‐methyladenosine, A m . A m may then be subjected to an additional methylation to form m 6 A m . Although initial mapping technologies could not discriminate between m 6 A and m 6 A m , we developed miCLIP, a single‐nucleotide resolution mapping technique that definitively discriminates between these highly abundant modifications. We find m 6 A and m 6 A have different effects on mRNA. m 6 A has diverse effects on transcripts, and when found in the 5′ untranslated region, can divert transcripts into a new form of translation that bypasses normal cap‐binding proteins. This form of m 6 A‐regulated translation appears to promote translation of specific mRNAs, especially in disease‐states associated with inhibition of cap‐binding proteins. In addition, we find that m 6 A influences the subcellular localization of transcripts in normal and disease cells. In contrast, we find that m 6 A m primarily enhances mRNA stability and translation. m 6 A m ‐initiated transcripts are markedly more stable due to resistance to the mRNA‐decapping enzyme DCP2. m 6 A m promotes translation via recruitment of specific m 6 A m ‐binding proteins leading to a unique form of translation initiation, that like m6A, does not require conventional cap‐binding proteins. Notably, m 6 A m can be demethylated to A m by FTO (fat mass and obesity‐associated protein). FTO was previously thought to demethylate m 6 A; however, FTO shows a markedly higher activity towards m 6 A m compared to m 6 A in vitro and no detectable demethylation of m 6 A in vivo . FTO demethylates m 6 A m to A m , and thereby switches off the stability of these transcripts. Overall, our findings reveal that epitranscriptomic information is stored in both internal nucleotides and mRNAs caps, with the “cap epitranscriptome” defining a novel reversible form of methylation that influences a large subset of cellular transcripts. Support or Funding Information Supported by the National Institutes of Health This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .